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treangenlab / Olivar

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
https://doi.org/10.1038/s41467-024-49957-9
GNU General Public License v3.0
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The progress bar remains at 0% without any changes. #21

Closed wangzhichao1990 closed 5 days ago

wangzhichao1990 commented 5 days ago

Hi, I run olivar on Bordetella pertussis genome. However, The progress bar remains at 0% without any changes. image

Is this software suitable for bacterial genomes? Will the genome be too large to make this plan applicable.

mxwang66 commented 5 days ago

Hi @wangzhichao1990 , thanks for reaching out! Based on your inputs you would expect ~1000 amplicons, and that well exceeds the limit of regular multiplex PCR. So you might need to trim down your input sequence.

For the progress bar sticking at 0, most likely it's because there are too many amplicons to design. You can try adding more threads and wait for a longer time. It will only increase by 10% each time. You may also add "nohup" to the start of your command so you won't have to keep the shell session running.

Let me know if you have any questions!

Michael

wangzhichao1990 commented 5 days ago

Thanks for your reply. I run in tmux window. Maybe I should use probes to capture large genomes.